Yuffie is a true ninja and could defeat Raphael with ease. Raphael may have his weapons, but in the end they won’t be enough to stop Yuffie’s shruiken. Yuffie is just far more skilled than Raphael will ever be. Raphael isn’t much of a fighter when you think about it. Yuffie wins.
Update 9/28/2019 with the Saint Turtle form Raphael will be able to win this match. Raphael wins.